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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtccgtgctatcccattccatttcgtagtttctactatttcccattgtttcatttcattcgatgattatgctccgattgaagCAGCTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAAGCTATAGCTAATAGTCCGCTAGGGGAGTCGCTTCAGAGGAAAATGGAGG

Basic information

species Glycine max
transcript GLYMA17G38220.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G38220.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0122g00430.t01 (Vitis vinifera), 3'ss of exon 1
gtccgtgctatcccattccatttcgtagtttctactatttccc--attgtttcatttcattcgatgattatgctccgattgaagCAGCTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAAGCTATAGCTAATAGTCCGCTAGGGGAGTCGCTTCAGAGGAAAATGGAGG---
||| | |   | | |     |||| | || ||  ||  || |   | |||   | ||   || |     ||  |    ||   | ||||||| || |||||| ||||||| |||||||||||||| ||||| ||||| ||||| ||||| || || || ||||||||||||||   ||||||||   
gtctgcgaatttctagg--gtttctttgtctcctctcgtttcagaactgtgaaacttatctctacttacatttttttttttgggaagCTCGCCGGCGTTTTAATATTCTCAGCGATTCCTTTCACCGCCGTTAAAGCCATAGCGAATAGCCCTCTCGGAGAGTCGCTTCAGAGCCGAATGGAGGAGA
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|208074776|gb|GD869547.1|GD869547
EST:     CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGCAAGAG                         C---TCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAA
genomic: CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGCAAGAGgtccgtgcta ... ccgattgaagCAGCTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAA
EST: gi|120491971|gb|EH220138.1|EH220138
EST:     CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGC-A-AG                         -AGCTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAA
genomic: CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGCAAGAGgtccgtgcta ... ccgattgaagCAGCTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAA
EST: gi|151404020|gb|EV273830.1|EV273830
EST:     CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGC-A-AG                         -AGCTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAA
genomic: CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGCAAGAGgtccgtgcta ... ccgattgaagCAGCTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAA
EST: gi|209716259|gb|BW657562.1|BW657562
EST:     CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGC-A-AG                         -AGCTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAA
genomic: CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGCAAGAGgtccgtgcta ... ccgattgaagCAGCTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAA
EST: gi|10846954|gb|BF069679.1|BF069679
EST:     CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGC-A-AG                         -AGCTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAA
genomic: CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGCAAGAGgtccgtgcta ... ccgattgaagCAGCTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAA
EST: gi|15285088|gb|BI468979.1|BI468979
EST:     CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGC-A-AG                         -AGCTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAA
genomic: CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGCAAGAGgtccgtgcta ... ccgattgaagCAGCTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAA
EST: gi|151395535|gb|EV265412.1|EV265412
EST:     CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGC-A-AG                         -AGCTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAA
genomic: CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGCAAGAGgtccgtgcta ... ccgattgaagCAGCTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAA
EST: gi|207796870|gb|GD770248.1|GD770248
EST:     CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGCAAGAG                         C---TCGCGGGAGTTTTACTATTCTCCGCGATTCCATTCACTGCCGTGAAA
genomic: CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGCAAGAGgtccgtgcta ... ccgattgaagCAGCTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAA
EST: gi|22539788|gb|BU089631.1|BU089631
EST:     CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGC-A-AG                         -AGCTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAA
genomic: CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGCAAGAGgtccgtgcta ... ccgattgaagCAGCTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAA
EST: gi|120533754|gb|EH261887.1|EH261887
EST:     CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGCAAGAG                         CAGCTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAA
genomic: CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGCAAGAGgtccgtgcta ... ccgattgaagCAGCTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAA
EST: gi|209703879|gb|BW667920.1|BW667920
EST:     CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGC-A-AG                         -AGCTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAA
genomic: CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGCAAGAGgtccgtgcta ... ccgattgaagCAGCTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAA
EST: gi|20075945|gb|BQ094728.1|BQ094728
EST:     CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGC-A-AG                         -AGCTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAA
genomic: CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGCAAGAGgtccgtgcta ... ccgattgaagCAGCTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAA
EST: gi|6727137|gb|AW311491.1|AW311491
EST:     CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGC-A-AG                         -AGCTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAA
genomic: CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGCAAGAGgtccgtgcta ... ccgattgaagCAGCTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAA
EST: gi|22540334|gb|BU090177.1|BU090177
EST:     CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGC-A-AG                         -AGCTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAA
genomic: CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGCAAGAGgtccgtgcta ... ccgattgaagCAGCTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAA
EST: gi|209714192|gb|BW679521.1|BW679521
EST:     CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGC-A-AG                         -AGCTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAA
genomic: CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGCAAGAGgtccgtgcta ... ccgattgaagCAGCTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAA
EST: gi|151404614|gb|EV274428.1|EV274428
EST:     CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGC-A-AG                         -AGCTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAA
genomic: CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGCAAGAGgtccgtgcta ... ccgattgaagCAGCTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAA
EST: gi|192297292|gb|FG990626.1|FG990626
EST:     CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGC-A-AG                         -AGCTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAA
genomic: CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGCAAGAGgtccgtgcta ... ccgattgaagCAGCTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAA
EST: gi|209718155|gb|BW677426.1|BW677426
EST:     CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGC-A-AG                         -AGCTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAA
genomic: CTGCCCCGAAGCGAAGAAGAAGCAGCTTCATTACTGCTTCGTGGCAAGAGgtccgtgcta ... ccgattgaagCAGCTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttctactatttcccattgtttcatttcattcgatgattatgctccgattgaagCAGCTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAAGCTATAGCTAATAGTCCGCTAGGGGAGTCGCTTCAGAGGAAAATGGAGG
     tactattt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtccgtgctatcccattccatttcgtagtttctactatttcccattgtttcatttcattcgatgattatgctccgattgaagCAGCTCGCGGGAGTTTTACTATTCTCCGCGATTCCTTTCACTGCCGTGAAAGCTATAGCTAATAGTCCGCTAGGGGAGTCGCTTCAGAGGAAAATGGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG